MSnID (version 1.6.0)

assess_termini: Checks if the peptide termini conforms with cleavage specificity

Description

Bottom-up proteomics approaches utilize endoproteases or chemical agents to digest proteins into smaller fragments called peptides. The enzymes recognize short amino acid motifs and cleave along the peptide bonds. Chemical agents such as CNBr also possesses amino acid cleavage specificity.

This function checks if peptide termini are as expected given the enzymatic/chemical cleavage specificity. The default value for validCleavagePattern is [KR]\.[^P], which corresponds to trypsin.

Usage

assess_termini(object, validCleavagePattern="[KR]\\.[^P]")

Arguments

object

An instance of class "MSnID".

validCleavagePattern

Cleavage pattern in the form of regular expression.

Value

Returns an instance of "MSnID" class with additional column "numIrregCleavages". If both termini conforms with cleavage specificity, then value is 0, if one or two termini are irregular then the values are 1 and 2, correspondingly.

Warning

If the "MSnID" instance does not contain "peptide" column in MS/MS results table then there will be an error. E.g. you can check this by "peptide" %in% names(msnid) where msnid is your "MSnID" instance.

Details

N- or C- protein termini are not considered as irregular clevages sites.

See Also

assess_missed_cleavages

Examples

data(c_elegans)
# adding column numIrregCleavages 
# containing count of irregularly cleaved termini
msnidObj <- assess_termini(msnidObj, validCleavagePattern="[KR]\\.[^P]")
# check the distribution
table(msnidObj$numIrregCleavages)